Oligonucleotide Based-Biosensors for Label-Free Electrochemical Protein and DNA Detection.

In the last years, DNA arrays have attracted increasing attention among medical diagnosis and analytical chemists. The broad range of application that has been found for DNA arrays makes them an important analytical tool. DNA arrays are relevant for the diagnosis of genetic diseases, detection of infectious agents, study of genetic predisposition, development of a personalised medicine, detection of differential genetic expression, forensic science, drug screening, food safety and environmental monitoring.Despite the great promise of DNA arrays in health care and their success in medical and biological research, the technology is still far away from the daily use in the clinic and even more far away from their implementation in home-diagnosis such as glucose biosensors. Their principal problems are the high cost and difficulty of use, because it is required costly laboratory instruments and biology knowledge for the labelling of the DNA prior to the sample injection into the array.On the other hand, the requirements that a biosensor should include are to be easy-to use so that it do not need the previous label of the sample and the addition of reagents. It should give a sensitive response in short time, and it should also include cheap generic multi-analyte detection.The work carried out in this thesis describes new concepts of electrochemical biosensoric platforms based on oligonucleotides for detection of label-free DNA and protein, which include these requirements.Preliminary experiments of direct DNA electrochemical detection of labelled ssDNA were performed to establish a protocol of DNA immobilisation, hybridisation and detection colourimetrically and electrochemically. DNA real samples and multi-analite detection on an array developed by biocopatible photolithography were used.To avoid the analyte labelling to develop an easy to use and low cost device, a label-free electrochemical displacement of DNA sensor was described. The method of detection by displacement requires the pre-hybridisation of the capture probe immobilised on the electrode surface with a sub-optimum mutated oligonucleotide labelled with a redox molecule. Due to the higher affinity of the target that is fully complementary to the capture probe, the sub-optimum label can be displaced when the complementary target is introduced in the system. The decrease of the signal would verify the presence of the target and should be proportional to its concentration. Sub-optimum hybridisation displacement detection was demonstrated colourimetrically and electrochemically with a sub-optimum mutated oligonucleotide labelled with horseradish peroxidase (HRP), and a ferrocene sub-optimum mutated oligonucleotide was also detected electrochemically, which do not required the addition of reagents for its detection.Furthermore different strategies to develop an electrochemical oligonucleotide (aptamer) based sensor for reagentless and label-free protein detection was carried out. The most sensitive aptasensor achieved 30 fM of detection limit in just 5 minutes.En els últims anys, els xips d'ADN han atret una atenció creixen en els camps de la diagnosis mèdica i la química analítica, degut a la seva portabilitat, sensibilitat, especificitat, ràpida resposta i l'ampli ventall d'aplicacions. Els xips d'ADN són rellevants per la diagnosis de malalties genètiques, detecció d'agents infecciosos, estudis de predisposició genètica, desenvolupament de medicina personalitzada, detecció d'expressió genètica diferencial, medicina forense, exploració de medicaments, seguretat alimentaria, defensa militar i monitorització mediambiental. Encara que els xips basats en oligonucleòtids per la detecció d'ADN i proteïnes siguin una gran promesa en medicina i recerca biològica, aquesta tecnologia es encara molt lluny del seu ús diari en el camp clínic i encara més lluny de poder ser comercialitzada per ús domèstic com ho han estat el biosensors de glucosa. Els seus principals problemes són el seu alt cost i la seva dificultat d'ús. Ja que per la seva utilització és necessari, previ a la injecció de l'analit en el biosensor, costosos instruments de laboratori i tècnics especialitzats en bioquímica pel marcatge i amplificació de les mostres d'ADN. En canvi els requeriments que un biosensor ha d'incloure són, ser fàcil d'utilitzar, per tant que l'analit no necessiti un marcatge previ i l'addició de reactius per la seva detecció. Aquest ha de donar una resposta ràpida i sensible a baix cost i ha de permetre la detecció en el mateix equip de diferent tipus d'analits.El treball fet en aquesta tesis descriu el desenvolupament de nous concepte de plataformes biosensòriques electroquímiques basades en oligonucleòtids per la detecció d'ADN i proteïnes no marcades prèviament, els quals inclouen aquest requeriments. Experiments preliminars per la detecció de l'hibridació d'ADN marcat es van portar a fi per tal d'establir un protocol per la immobilització, hibridació i detecció d'ADN colorimètricament i electroquímicament. És van utilitzar mostres reals d'ADN i sistemes de detecció de multi-analits en un xip desenvolupat per fotolitografia biocompatible.Per tal de no necessitar un marcatge previ de la mostres d'ADN i així simplificar i reduir el cost del futur biosensor es va desenvolupar un sistema electroquímic de desplaçament. El mètode lliure de marcatge es basa en el desplaçament de molècules d'oligonucleòtid mutat i marcat, els quals encara que continguin certes mutacions són capaços d'hibridar amb la sonda d'oligonucleòtid immobilitzat, però quan aquestes es troben en presència de l'analit desplaça la molècula mutada i marcada, disminuint així la senyal de manera proporcional en la concentració del analit. El sistema de desplaçament ha estat demostrat colorimètricament i electroquímicament utilitzant un marcatge d'HRP sobre el mutat i utilitzant un marcatge de ferrocè en l'oligonucleòtid mutat per tal de no necessitar afegir cap reactiu per la detecció de l'analit, També es van portar a fi diferents estratègies per desenvolupar un biosensor electroquímic basat en oligonucleòtids (aptamers) per la detecció de la proteïna trombina sense el previ marcatge d'aquest analit i sense necessitat d'afegir reactius per la detecció del analit. En el sistema mes sensible es va obtenir un límit de detecció de 30 fM en un temps de resposta de sols 5 minuts.En los últimos años, los chips de ADN han atraído una atención creciente diferentes campos, debido a su portabilidad, sensibilidad, especificidad y rápida respuesta. Los chips de ADN son aplicados en diagnosis de enfermedades genéticas, detección de agentes infecciosos, estudios de predisposición genética, desarrollo de medicina personalizada, detección de expresión genética diferencial, medicina forense, exploración de medicamentos, columnas de separación, seguridad alimentaría, defensa militar y monitorización medioambiental. Aunque los chips basados en oligonucleótidos para la detección de ADN y proteínas tienen un gran futuro en diagnosis e investigación biológica, esta tecnología está aun muy lejos de su uso diario en el campo clínico y aun mas lejos de poder ser comercializado para uso doméstico como lo han sido los biosensores de glucosa. Sus principales problemas son su alto coste y su dificultad de uso. Para su utilización es necesario, previo a la inyección del analito en el biosensor, costosos instrumentos de laboratorio y técnicos especializados en bioquímica para el marcaje y amplificación de las muestras de ADN. En cambio los requerimientos que un biosensor ha de incluir son, ser fácil de utilizar, por tanto el analito no ha de necesitar un marcaje previo ni la adición de reactivos para su detección. Este ha de dar una respuesta rápida y sensible a bajo coste y ha de permitir la detección en el mismo equipo de diferentes analitos.El trabajo hecho en esta tesis describe el desarrollo de nuevos conceptos de plataformas biosensóricas electroquímicas basadas en oligonucleótidos para la detección de ADN y proteínas no marcadas previamente, los cuales incluyen estos requerimientos.Experimentos preliminares para la detección directa de la hibridación de ADN marcado se llevó a cabo para establecer protocolos para la inmovilización, hibridación y detección de ADN colorimétricamente y electroquímicamente. Se utilizaron muestras reales y sistemas de detección de multi-analitos en un chip desarrollado por fotolitografía biocompatible.Para no necesitar un marcaje previo de la muestra de ADN y así simplificar y reducir el coste del futuro biosensor se desarrolló un sistema electroquímico de desplazamiento. El método libre de marcaje se basa en el desplazamiento de moléculas de oligonucleótido mutado y marcado, el cual aunque contenga ciertas mutaciones es capaz de hibridar con la sonda de oligonucleótido inmovilizado, pero cuando estas se encuentran en presencia del analito desplaza la molécula mutada, disminuyendo así la señal de manera proporcional a la concentración del analito. El sistema de desplazamiento ha sido demostrado colorimétricamente y electroquímicamente utilizando marcaje de HRP sobre el mutado, así como un marcaje de ferroceno que no requiere la adición de reactivos para su detección. También se llevaron a cabo diferentes estrategias para desarrollar un biosensor electroquímico basado en oligonucleótidos (aptámeros) para la detección de trombina sin el previo marcaje de este analito, ni la adición de reactivos para la detección del analito. En el sistema más sensible se obtuvo un límite de detección de 30 fM en un tiempo de respuesta de solo 5 minuto

Simple and fast method for fabrication of endoscopic implantable sensor arrays

Here we have developed a simple method for the fabrication of disposable implantable all-solid-state ion-selective electrodes (ISE) in an array format without using complex fabrication equipment or clean room facilities. The electrodes were designed in a needle shape instead of planar electrodes for a full contact with the tissue. The needle-shape platform comprises 12 metallic pins which were functionalized with conductive inks and ISE membranes. The modified microelectrodes were characterized with cyclic voltammetry, scanning electron microscope (SEM), and optical interferometry. The surface area and roughness factor of each microelectrode were determined and reproducible values were obtained for all the microelectrodes on the array. In this work, the microelectrodes were modified with membranes for the detection of pH and nitrate ions to prove the reliability of the fabricated sensor array platform adapted to an endoscope

Miniaturizable ion-selective arrays based on highly stable polymer membranes for biomedical applications

Poly(vinylchloride) (PVC) is the most common polymer matrix used in the fabrication of ion-selective electrodes (ISEs). However, the surfaces of PVC-based sensors have been reported to show membrane instability. In an attempt to overcome this limitation, here we developed two alternative methods for the preparation of highly stable and robust ion-selective sensors. These platforms are based on the selective electropolymerization of poly(3,4-ethylenedioxythiophene) (PEDOT), where the sulfur atoms contained in the polymer covalently interact with the gold electrode, also permitting controlled selective attachment on a miniaturized electrode in an array format. This platform sensor was improved with the crosslinking of the membrane compounds with poly(ethyleneglycol) diglycidyl ether (PEG), thus also increasing the biocompatibility of the sensor. The resulting ISE membranes showed faster signal stabilization of the sensor response compared with that of the PVC matrix and also better reproducibility and stability, thus making these platforms highly suitable candidates for the manufacture of robust implantable sensors. Keywords: ion-selective electrode (ISE) sensor, pH detection, ischemia, electrochemistry, implantable device, biomedicine, endoscop

Sensor-integrated microfluidic approaches for liquid biopsies applications in early detection of cancer

Cancer represents one of the conditions with the most causes of death worldwide. Common methods for its diagnosis are based on tissue biopsies the extraction of tissue from the primary tumor, which is used for its histological analysis. However, this technique represents a risk for the patient, along with being expensive and time-consuming and so it cannot be frequently used to follow the progress of the disease. Liquid biopsy is a new cancer diagnostic alternative, which allows the analysis of the molecular information of the solid tumors via a body fluid draw. This fluid-based diagnostic method displays relevant advantages, including its minimal invasiveness, lower risk, use as often as required, it can be analyzed with the use of microfluidic-based platforms with low consumption of reagent, and it does not require specialized personnel and expensive equipment for the diagnosis. In recent years, the integration of sensors in microfluidics lab-on-a-chip devices was performed for liquid biopsies applications, granting significant advantages in the separation and detection of circulating tumor nucleic acids (ctNAs), circulating tumor cells (CTCs) and exosomes. The improvements in isolation and detection technologies offer increasingly sensitive and selective equipment's, and the integration in microfluidic devices provides a better characterization and analysis of these biomarkers. These fully integrated systems will facilitate the generation of fully automatized platforms at low-cost for compact cancer diagnosis systems at an early stage and for the prediction and prognosis of cancer treatment through the biomarkers for personalized tumor analysis

Biosensors Integration in blood-brain barrier-on-a-chip: emerging platform for monitoring neurodegenerative diseases

Over the most recent decades, the development of new biological platforms to study disease progression and drug efficacy has been of great interest due to the high increase in the rate of neurodegenerative diseases (NDDs). Therefore, blood–brain barrier (BBB) as an organ-on-a-chip (OoC) platform to mimic brain-barrier performance could offer a deeper understanding of NDDs as well as a very valuable tool for drug permeability testing for new treatments. A very attractive improvement of BBB-oC technology is the integration of detection systems to provide continuous monitoring of biomarkers in real time and a fully automated analysis of drug permeably, rendering more efficient platforms for commercialization. In this Perspective, an overview of the main BBB-oC configurations is introduced and a critical vision of the BBB-oC platforms integrating electronic read out systems is detailed, indicating the strengths and weaknesses of current devices, proposing the great potential for biosensors integration in BBB-oC. In this direction, we name potential biomarkers to monitor the evolution of NDDs related to the BBB and/or drug cytotoxicity using biosensor technology in BBB-oC

Neurovascular unit on a chip: the relevance and maturity as an advanced in vitro model

[No abstract available

DNA-origami-aided lithography for sub-10 nanometer pattern printing

We report the first DNA-based origami technique that can print addressable patterns on surfaces with sub-10 nm resolution. Specifically, we have used a two-dimensional DNA origami as a template (DNA origami stamp) to transfer DNA with pre-programmed patterns (DNA ink) on gold surfaces. The DNA ink is composed of thiol-modified staple strands incorporated at specific positions of the DNA origami stamp to create patterns upon thiol-gold bond formation on the surface (DNA ink). The DNA pattern formed is composed of unique oligonucleotide sequences, each of which is individually addressable. As a proof-of-concept, we created a linear pattern of oligonucleotide-modified gold nanoparticles complementary to the DNA ink pattern. We have developed an in silico model to identify key elements in the formation of our DNA origami-driven lithography and nanoparticle patterning as well as simulate more complex nanoparticle patterns on surfaces

Non-invasive monitoring of pH and oxygen using miniaturized electrochemical sensors in an animal model of acute hypoxia

Background: One of the most prevalent causes of fetal hypoxia leading to stillbirth is placental insufficiency. Hemodynamic changes evaluated with Doppler ultrasound have been used as a surrogate marker of fetal hypoxia. However, Doppler evaluation cannot be performed continuously. As a first step, the present work aimed to evaluate the performance of miniaturized electrochemical sensors in the continuous monitoring of oxygen and pH changes in a model of acute hypoxia-acidosis. Methods: pH and oxygen electrochemical sensors were evaluated in a ventilatory hypoxia rabbit model. The ventilator hypoxia protocol included 3 differential phases: basal (100% FiO2), the hypoxia-acidosis period (10% FiO2) and recovery (100% FiO2). Sensors were tested in blood tissue (ex vivo sensing) and in muscular tissue (in vivo sensing). pH electrochemical and oxygen sensors were evaluated on the day of insertion (short-term evaluation) and pH electrochemical sensors were also tested after 5 days of insertion (long-term evaluation). pH and oxygen sensing were registered throughout the ventilatory hypoxia protocol (basal, hypoxia-acidosis, and recovery) and were compared with blood gas metabolites results from carotid artery catheterization (obtained with the EPOC blood analyzer). Finally, histological assessment was performed on the sensor insertion site. One-way ANOVA was used for the analysis of the evolution of acid-based metabolites and electrochemical sensor signaling results; a t-test was used for pre- and post-calibration analyses; and chi-square analyses for categorical variables. Results: At the short-term evaluation, both the pH and oxygen electrochemical sensors distinguished the basal and hypoxia-acidosis periods in both the in vivo and ex vivo sensing. However, only the ex vivo sensing detected the recovery period. In the long-term evaluation, the pH electrochemical sensor signal seemed to lose sensibility. Finally, histological assessment revealed no signs of alteration on the day of evaluation (short-term), whereas in the long-term evaluation a sub-acute inflammatory reaction adjacent to the implantation site was detected. Conclusions: Miniaturized electrochemical sensors represent a new generation of tools for the continuous monitoring of hypoxia-acidosis, which is especially indicated in high-risk pregnancies. Further studies including more tissue-compatible material would be required in order to improve long-term electrochemical sensing

Miniaturized Electrochemical Sensors to Monitor Fetal Hypoxia and Acidosis in a Pregnant Sheep Model

Perinatal asphyxia is a major cause of severe brain damage and death. For its prenatal identification, Doppler ultrasound has been used as a surrogate marker of fetal hypoxia. However, Doppler evaluation cannot be performed continuously. We have evaluated the performance of a miniaturized multiparametric sensor aiming to evaluate tissular oxygen and pH changes continuously in an umbilical cord occlusion (UCO) sheep model. The electrochemical sensors were inserted in fetal hindlimb skeletal muscle and electrochemical signals were recorded. Fetal hemodynamic changes and metabolic status were also monitored during the experiment. Additionally, histological assessment of the tissue surrounding the sensors was performed. Both electrochemical sensors detected the pO2 and pH changes induced by the UCO and these changes were correlated with hemodynamic parameters as well as with pH and oxygen content in the blood. Finally, histological assessment revealed no signs of alteration on the same day of insertion. This study provides the first evidence showing the application of miniaturized multiparametric electrochemical sensors detecting changes in oxygen and pH in skeletal muscular tissue in a fetal sheep model.This research was funded by CELLEX FOUNDATION. This work was financially supported by The Cellex Foundation and the Agència de Gestió d’Ajuts Universitaris i de Recerca (Grant 2017 SGR 1531). Additionally, E.E. has received support from the Departament de Salut (Grant SLT008/18/00156). The Nanobioengineering group at the Institute of Bioengineering of Catalonia (IBEC) has received support from the Commission for Universities and Research of the Department of Innovation, Universities, and Enterprise of the Generalitat de Catalunya (No. 2017 SGR 1079) and is part of the CERCA Programme / Generalitat de Catalunya and is supported by the Severo Ochoa programme of the Spanish Ministry of Science and Competitiveness (Grant SEV-2014-0425 (2015–2019)). CIBER-BBN is an initiative funded by the VI National R&D&i Plan 2008–2011, Iniciativa Ingenio 2010, Consolider Program, CIBER Actions and financed by the Instituto de Salud Carlos III with assistance from the European Regional Development Fund. L.R. would also like to acknowledge her support within the BEST Postdoctoral Programme, funded by the European Commission under Horizon 2020’s Marie Skłodowska-Curie Actions COFUND scheme (Grant Agreement No. 712754)

Micro-needle implantable electrochemical oxygen sensor: ex-vivo and in-vivo studies

Oxygen is vital for energy metabolism in mammals and the variability of the concentration is considered a clinical alert for a wide range of metabolic malfunctions in medicine. In this article, we describe the development and application of a micro-needle implantable platinum-based electrochemical sensor for measuring partial pressure of oxygen in intramuscular tissue (in-vivo) and vascular blood (ex-vivo). The Pt-Nafion® sensor was characterized morphological and electrochemically showing a higher sensitivity of -2.496 nA/mmHg (-1.495 nA/μM) when comparing with its bare counterpart. Our sensor was able to discriminate states with different oxygen partial pressures (pO2) for ex-vivo (blood) following the same trend of the commercial gas analyzer used as standard. For in-vivo (intramuscular) experiments, since there is not a gold standard for measuring pO2 in tissue, it was not possible to correlate the obtained currents with the pO2 in tissue. However, our sensor was able to detect clear statistical differences of O2 between hyperoxia and hypoxia states in tissue